Not sure which one you plan to do, but I found this:
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I'm not entirely sure, but as far as I can tell, the 3 BCs accessed with the "Confidential Imperial Order" are still capped, but the 3 with accessed with the "Secret Imperial Order" are not. I can check tomorrow.
The Secret Imperial order ISNMs were never capped, but the level 60 ISNMs likely will still be capped, as they never uncapped any of the optional/reward-based BCNMs.